Summary

Bio::Tools::Tmhmm - parse TmHMM output (transmembrane HMM)

Package variables

Included modules

Inherit

Bio::Root::IO Bio::Root::Root Bio::Tools::AnalysisResult

Synopsis

  use Bio::Tools::Tmhmm;
  my $parser = new Bio::Tools::Tmhmm(-fh =>$filehandle );
  while( my $tmhmm_feat = $parser->next_result ) {
     #do something
     #eg
     push @tmhmm_feat, $tmhmm_feat;
  }

Description

Parser for Tmhmm output

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Tools::Tmhmm();
 Function: Builds a new Bio::Tools::Tmhmm object
 Returns : Bio::Tools::Tmhmm
 Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO

 Title   : next_result
 Usage   : my $feat = $Tmhmm->next_result
 Function: Get the next result set from parser data
 Returns : Bio::SeqFeature::Generic
 Args    : none

 Title   : create_feature
 Usage   : obj->create_feature(\%feature)
 Function: Internal(not to be used directly)
 Returns : A Bio::SeqFeature::Generic object
 Args    :

 Title   :   _seqname
 Usage   :   obj->_seqname($seqname)
 Function:   Internal(not to be used directly)
 Returns :
 Args    :   seqname

Methods code

sub new {

      my($class,@args) = @_;

      my $self = $class->SUPER::new(@args);
      $self->_initialize_io(@args);

      return $self;

}

sub next_result {

        my ($self) = @_;

        my $line;

        # parse
        my $id;
        while ($_=$self->_readline()) { 
           $line = $_;
           chomp $line;


           next if /^$/;
           if ($line=~/^#\s+(\S+)/) { 
                   #if the line starts with a '#' for example in # 13 Length: 522 
                   #assign 13 as the id.

                    $id = $1;
                    my ($junk, $values) = split /:/;
                   $self->_seqname($id);
                    next;
           }

           elsif ($line=~/^(\S+)\s+(\S+)\s+(\w+)\s+(\d+)\s+(\d+)/) {

                    # Example :-  13      TMHMM2.0        inside       1   120
                    # assign $orien(inside) $start(1) and $end(120)


                    my $orien = $3;
                    my $start = $4;
                    my $end = $5;
                    $orien = uc ($orien);

                    if ($orien eq "TMHELIX") {
                         my (%feature);
                         $feature{name} = $self->_seqname;
                         $feature{start} = $start;
                         $feature{end} = $end;
                         $feature{source} ='tmhmm';
                         $feature{primary}= 'transmembrane';
                         $feature{program} ='tmhmm';
                         $feature{logic_name} = 'TMHelix';
                         my $new_feat= $self->create_feature(\%feature);
                         return $new_feat;
                    }
                    next;
           }
           next;
        }

}

sub create_feature {

       my ($self, $feat) = @_;


       # create feature object
       my $feature = Bio::SeqFeature::Generic->new(-seq_id => $feat->{name},
                                                 -start    => $feat->{start},
                                                 -end      => $feat->{end},
                                                 -score    => $feat->{score},
                                                 -source   => $feat->{source},
                                                 -primary  => $feat->{primary},
                                                 -logic_name  => $feat->{logic_name}, 
                                               );
       return $feature;

}

sub _seqname {

    my ($self,$seqname)=@_;

    if (defined $seqname){

        $self->{'seqname'}=$seqname;
    }

    return $self->{'seqname'};

}

General documentation

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The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _